When running the test app below you get a NPE thrown at the start. I expect this is because it starts changing the data before the chart is 100% built, but we need to defend against the NPE error.

java.lang.NullPointerException
      at javafx.scene.chart.LineChart.dataItemRemoved(LineChart.java:168)
      at javafx.scene.chart.XYChart.dataItemsChanged(XYChart.java:306)
      at javafx.scene.chart.XYChart.access$2500(XYChart.java:35)
      at javafx.scene.chart.XYChart$Series$1.onChanged(XYChart.java:1122)
      at com.sun.javafx.collections.ObservableListWrapper.callObservers(ObservableListWrapper.java:62)
      at com.sun.javafx.collections.ObservableListWrapper.set(ObservableListWrapper.java:196)
      at base$1.handle(base.java:35)
      at base$1.handle(base.java:1)
      at com.sun.scenario.animation.shared.TimelineClipCore.visitKeyFrame(TimelineClipCore.java:185)
      at com.sun.scenario.animation.shared.TimelineClipCore.playTo(TimelineClipCore.java:132)
      at javafx.animation.Timeline.impl_playTo(Timeline.java:144)
      at com.sun.scenario.animation.shared.GeneralClipEnvelope.visitCycle(GeneralClipEnvelope.java:255)
      at com.sun.scenario.animation.shared.GeneralClipEnvelope.timePulse(GeneralClipEnvelope.java:184)
      at javafx.animation.Animation.impl_timePulse(Animation.java:795)
      at com.sun.scenario.animation.shared.AnimationPulseReceiver.timePulse(AnimationPulseReceiver.java:83)
      at com.sun.scenario.animation.AbstractMasterTimer.timePulseImpl(AbstractMasterTimer.java:332)
      at com.sun.scenario.animation.AbstractMasterTimer$MainLoop.run(AbstractMasterTimer.java:245)
      at com.sun.javafx.tk.quantum.QuantumToolkit.pulse(QuantumToolkit.java:340)
      at com.sun.javafx.tk.quantum.QuantumToolkit$9.run(QuantumToolkit.java:284)
      at com.sun.glass.ui.win.WinApplication._runLoop(Native Method)
      at com.sun.glass.ui.win.WinApplication.access$100(WinApplication.java:29)
      at com.sun.glass.ui.win.WinApplication$1$1.run(WinApplication.java:49)
      at java.lang.Thread.run(Unknown Source)
 



import javafx.animation.Animation;
import javafx.animation.KeyFrame;
import javafx.animation.Timeline;
import javafx.application.Application;
import javafx.event.ActionEvent;
import javafx.event.EventHandler;
import javafx.scene.Scene;
import javafx.scene.chart.LineChart;
import javafx.scene.chart.NumberAxis;
import javafx.scene.chart.XYChart;
import javafx.stage.Stage;
import javafx.util.Duration;

public class LineChartLeakTest extends Application {

    @Override public void start(Stage stage) throws Exception {
        LineChart<Number,Number> lineChart = new LineChart<Number, Number>(new NumberAxis(), new NumberAxis());
        // create single series with 50 items to start
        final LineChart.Series<Number,Number> series = new XYChart.Series<Number,Number>();
        for (int i=0; i< 50; i++) series.getData().add(new XYChart.Data<Number, Number>(Math.random(), Math.random()));
        lineChart.getData().add(series);

        stage.setScene(new Scene(lineChart,800,600));
        stage.setVisible(true);

        Timeline timeline = new Timeline();
        timeline.setCycleCount(Animation.INDEFINITE);
        timeline.getKeyFrames().add(new KeyFrame(new Duration(100), new EventHandler<ActionEvent>() {
            public void handle(ActionEvent actionEvent) {
                if (Math.random() < 0.9) { // 90% of the time replace a data item
                    if (!series.getData().isEmpty()) {
                        series.getData().set(
                            (int)(Math.random()*(series.getData().size()-1)),
                            new XYChart.Data<Number, Number>(Math.random(), Math.random())
                        );
                    }
                } else { // otherwise add a new data item
                    series.getData().add(new XYChart.Data<Number, Number>(Math.random(), Math.random()));
                }
            }
        }));
        timeline.play();
    }

    public static void main(String[] args) {
        launch(args);
    }
}